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- PDB-2h9h: An episulfide cation (thiiranium ring) trapped in the active site... -

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Basic information

Entry
Database: PDB / ID: 2h9h
TitleAn episulfide cation (thiiranium ring) trapped in the active site of HAV 3C proteinase inactivated by peptide-based ketone inhibitors
Components
  • Hepatitis A virus protease 3C
  • Three residue peptide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / METHYLKETONE / EPISULFIDE / HYDROLASE-HYDRLASE INHIBITOR COMPLEX / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / : / nucleoside-triphosphate phosphatase / protein complex oligomerization ...host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
: / 2B protein soluble domain / Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid ...: / 2B protein soluble domain / Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-acetyl-L-leucyl-L-alanyl-N-[(1S)-4-(dimethylamino)-1-(fluoroacetyl)-4-oxobutyl]-L-alaninamide / N-[(BENZYLOXY)CARBONYL]-L-ALANINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsYin, J. / Cherney, M.M. / Bergmann, E.M. / James, M.N.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: An Episulfide Cation (Thiiranium Ring) Trapped in the Active Site of HAV 3C Proteinase Inactivated by Peptide-based Ketone Inhibitors.
Authors: Yin, J. / Cherney, M.M. / Bergmann, E.M. / Zhang, J. / Huitema, C. / Pettersson, H. / Eltis, L.D. / Vederas, J.C. / James, M.N.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: Dual modes of modification of Hepatitis A virus 3C protease by a Serine-derived beta-lactone: selective crystallization and formation of a functional catalytic triad in the active site
Authors: Yin, J. / Bergmann, E.M. / Cherney, M.M. / Lall, M.S. / Jain, R.P. / Vederas, J.C. / James, M.N.G.
History
DepositionJun 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hepatitis A virus protease 3C
I: Three residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9843
Polymers23,7602
Non-polymers2231
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-10 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.672, 56.055, 80.974
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological assembly is a monomer

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Components

#1: Protein Hepatitis A virus protease 3C


Mass: 23288.844 Da / Num. of mol.: 1 / Fragment: 3C PROTEINASE, RESIDUES 1520-1731 / Mutation: C24S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis A virus / Genus: Hepatovirus / Gene: 3C / Plasmid: pHAV-3CEX / Production host: Escherichia coli (E. coli) / Strain (production host): D1210
References: UniProt: P06441, UniProt: P08617*PLUS, picornain 3C
#2: Protein/peptide Three residue peptide


Type: Peptide-like / Class: Inhibitor / Mass: 471.567 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: N-acetyl-L-leucyl-L-alanyl-N-[(1S)-4-(dimethylamino)-1-(fluoroacetyl)-4-oxobutyl]-L-alaninamide
#3: Chemical ChemComp-BBL / N-[(BENZYLOXY)CARBONYL]-L-ALANINE / N-BENZYLOXYCARBONYL-L-SERINE-BETALACTONE


Mass: 223.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 297 K / pH: 7.5
Details: 2.5% PEG 8000, 1.5% Glycerol, 10mM tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115879
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 29, 2004
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115879 Å / Relative weight: 1
ReflectionResolution: 1.35→26.49 Å / Num. obs: 36919 / % possible obs: 81.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.7
Reflection shellResolution: 1.35→1.4 Å / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.6 / % possible all: 22.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A4O

2a4o


Resolution: 1.39→26.49 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.599 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1838 5.1 %RANDOM
Rwork0.181 ---
obs0.182 34294 86.7 %-
all-34342 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2---0.55 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.39→26.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 16 263 1946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221715
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9712313
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0085215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31524.92869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77315298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.304157
X-RAY DIFFRACTIONr_chiral_restr0.0810.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021266
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2794
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21194
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2186
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.89941096
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.90561725
X-RAY DIFFRACTIONr_scbond_it3.988692
X-RAY DIFFRACTIONr_scangle_it5.82910588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.39→1.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 60 -
Rwork0.329 1267 -
obs--43.51 %

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